1
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Kharchenko V, Al-Harthi S, Ejchart A, Jaremko Ł. Pitfalls in measurements of R 1 relaxation rates of protein backbone 15N nuclei. JOURNAL OF BIOMOLECULAR NMR 2024:10.1007/s10858-024-00449-4. [PMID: 39217275 DOI: 10.1007/s10858-024-00449-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Accepted: 08/08/2024] [Indexed: 09/04/2024]
Abstract
The dynamics of the backbone and side-chains of protein are routinely studied by interpreting experimentally determined 15N spin relaxation rates. R1(15N), the longitudinal relaxation rate, reports on fast motions and encodes, together with the transverse relaxation R2, structural information about the shape of the molecule and the orientation of the amide bond vectors in the internal diffusion frame. Determining error-free 15N longitudinal relaxation rates remains a challenge for small, disordered, and medium-sized proteins. Here, we show that mono-exponential fitting is sufficient, with no statistical preference for bi-exponential fitting up to 800 MHz. A detailed comparison of the TROSY and HSQC techniques at medium and high fields showed no statistically significant differences. The least error-prone DD/CSA interference removal technique is the selective inversion of amide signals while avoiding water resonance. The exchange of amide with solvent deuterons appears to affect the rate R1 of solvent-exposed amides in all fields tested and in each DD/CSA interference removal technique in a statistically significant manner. In summary, the most accurate R1(15N) rates in proteins are achieved by selective amide inversion, without the addition of D2O. Importantly, at high magnetic fields stronger than 800 MHz, when non-mono-exponential decay is involved, it is advisable to consider elimination of the shortest delays (typically up to 0.32 s) or bi-exponential fitting.
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Affiliation(s)
- Vladlena Kharchenko
- Biological and Environmental Science & Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Samah Al-Harthi
- Biological and Environmental Science & Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Andrzej Ejchart
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106, Warsaw, Poland
| | - Łukasz Jaremko
- Biological and Environmental Science & Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
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2
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Kharchenko V, Nowakowski M, Jaremko M, Ejchart A, Jaremko Ł. Dynamic 15N{ 1H} NOE measurements: a tool for studying protein dynamics. JOURNAL OF BIOMOLECULAR NMR 2020; 74:707-716. [PMID: 32918646 PMCID: PMC7701129 DOI: 10.1007/s10858-020-00346-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 08/12/2020] [Indexed: 06/11/2023]
Abstract
Intramolecular motions in proteins are one of the important factors that determine their biological activity and interactions with molecules of biological importance. Magnetic relaxation of 15N amide nuclei allows one to monitor motions of protein backbone over a wide range of time scales. 15N{1H} nuclear Overhauser effect is essential for the identification of fast backbone motions in proteins. Therefore, exact measurements of NOE values and their accuracies are critical for determining the picosecond time scale of protein backbone. Measurement of dynamic NOE allows for the determination of NOE values and their probable errors defined by any sound criterion of nonlinear regression methods. The dynamic NOE measurements can be readily applied for non-deuterated or deuterated proteins in both HSQC and TROSY-type experiments. Comparison of the dynamic NOE method with commonly implied steady-state NOE is presented in measurements performed at three magnetic field strengths. It is also shown that improperly set NOE measurement cannot be restored with correction factors reported in the literature.
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Affiliation(s)
- Vladlena Kharchenko
- Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Michal Nowakowski
- Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Mariusz Jaremko
- Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Andrzej Ejchart
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106, Warsaw, Poland
| | - Łukasz Jaremko
- Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
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3
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Bergkessel M, Babin BM, VanderVelde D, Sweredoski MJ, Moradian A, Eggleston-Rangel R, Hess S, Tirrell DA, Artsimovitch I, Newman DK. The dormancy-specific regulator, SutA, is intrinsically disordered and modulates transcription initiation in Pseudomonas aeruginosa. Mol Microbiol 2019; 112:992-1009. [PMID: 31254296 DOI: 10.1111/mmi.14337] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/25/2019] [Indexed: 11/27/2022]
Abstract
Though most bacteria in nature are nutritionally limited and grow slowly, our understanding of core processes like transcription comes largely from studies in model organisms doubling rapidly. We previously identified a small protein of unknown function, SutA, in a screen of proteins synthesized in Pseudomonas aeruginosa during dormancy. SutA binds RNA polymerase (RNAP), causing widespread changes in gene expression, including upregulation of the ribosomal RNA genes. Here, using biochemical and structural methods, we examine how SutA interacts with RNAP and the functional consequences of these interactions. We show that SutA comprises a central α-helix with unstructured N- and C-terminal tails, and binds to the β1 domain of RNAP. It activates transcription from the rrn promoter by both the housekeeping sigma factor holoenzyme (Eσ70 ) and the stress sigma factor holoenzyme (EσS ) in vitro, but has a greater impact on EσS . In both cases, SutA appears to affect intermediates in the open complex formation and its N-terminal tail is required for activation. The small magnitudes of in vitro effects are consistent with a role in maintaining activity required for homeostasis during dormancy. Our results add SutA to a growing list of transcription regulators that use their intrinsically disordered regions to remodel transcription complexes.
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Affiliation(s)
- Megan Bergkessel
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Brett M Babin
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - David VanderVelde
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Michael J Sweredoski
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA, USA
| | - Annie Moradian
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA, USA
| | - Roxana Eggleston-Rangel
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA, USA
| | - Sonja Hess
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA, USA
| | - David A Tirrell
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Irina Artsimovitch
- Department of Microbiology and The Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Dianne K Newman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.,Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
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4
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Jaremko Ł, Jaremko M, Ejchart A, Nowakowski M. Fast evaluation of protein dynamics from deficient 15N relaxation data. JOURNAL OF BIOMOLECULAR NMR 2018; 70:219-228. [PMID: 29594733 PMCID: PMC5953972 DOI: 10.1007/s10858-018-0176-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 03/20/2018] [Indexed: 06/08/2023]
Abstract
Simple and convenient method of protein dynamics evaluation from the insufficient experimental 15N relaxation data is presented basing on the ratios, products, and differences of longitudinal and transverse 15N relaxation rates obtained at a single magnetic field. Firstly, the proposed approach allows evaluating overall tumbling correlation time (nanosecond time scale). Next, local parameters of the model-free approach characterizing local mobility of backbone amide N-H vectors on two different time scales, S2 and R ex , can be elucidated. The generalized order parameter, S2, describes motions on the time scale faster than the overall tumbling correlation time (pico- to nanoseconds), while the chemical exchange term, R ex , identifies processes slower than the overall tumbling correlation time (micro- to milliseconds). Advantages and disadvantages of different methods of data handling are thoroughly discussed.
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Affiliation(s)
- Łukasz Jaremko
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Mariusz Jaremko
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Andrzej Ejchart
- Institute of Biochemistry and Biophysics, Polish Academy of Science, Pawinskiego 5A, 02-106, Warszawa, Poland
| | - Michał Nowakowski
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warszawa, Poland.
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5
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Langelaan DN, Pandey A, Sarker M, Rainey JK. Preserved Transmembrane Segment Topology, Structure, and Dynamics in Disparate Micellar Environments. J Phys Chem Lett 2017; 8:2381-2386. [PMID: 28492329 PMCID: PMC5770213 DOI: 10.1021/acs.jpclett.7b00867] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Detergent micelles are frequently employed as membrane mimetics for solution-state membrane protein nuclear magnetic resonance spectroscopy. Here we compare topology, structure, ps-ns time-scale dynamics, and hydrodynamics of a model protein with one transmembrane (TM) segment (residues 1-55 of the apelin receptor, APJ, a G-protein-coupled receptor) in three distinct, commonly used micellar environments. In each environment, two solvent-protected helical segments connected by a solvent-exposed kink were observed. The break in helical character at the kink was maintained in a helix-stabilizing fluorinated alcohol environment, implying that this structural feature is inherent. Molecular dynamics simulations also substantiate favorable self-assembly of compact protein-micelle complexes with a more dynamic, solvent-exposed kink. Despite the observed similarity in TM segment behavior, micelle-dependent differences were clear in the structure, dynamics, and compactness of the 30-residue, extramembrane N-terminal tail of the protein. This would affect intermolecular interactions and, correspondingly, the functional state of the membrane protein.
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Affiliation(s)
- David N. Langelaan
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax NS B3H 4R2, Canada
| | - Aditya Pandey
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax NS B3H 4R2, Canada
| | - Muzaddid Sarker
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax NS B3H 4R2, Canada
| | - Jan K. Rainey
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax NS B3H 4R2, Canada
- Department of Chemistry, Dalhousie University, Halifax NS B3H 4R2, Canada
- Corresponding author:
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6
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Soares PA, Queiroz IN, Pomin VH. NMR structural biology of sulfated glycans. J Biomol Struct Dyn 2016; 35:1069-1084. [DOI: 10.1080/07391102.2016.1171165] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Paulo A.G. Soares
- Program of Glycobiology, Institute of Medical Biochemistry Leopoldo de Meis, and University Hospital Clementino Fraga Filho, Federal University of Rio de Janeiro , Rio de Janeiro, RJ 21941-913, Brazil
| | - Ismael N.L. Queiroz
- Program of Glycobiology, Institute of Medical Biochemistry Leopoldo de Meis, and University Hospital Clementino Fraga Filho, Federal University of Rio de Janeiro , Rio de Janeiro, RJ 21941-913, Brazil
| | - Vitor H. Pomin
- Program of Glycobiology, Institute of Medical Biochemistry Leopoldo de Meis, and University Hospital Clementino Fraga Filho, Federal University of Rio de Janeiro , Rio de Janeiro, RJ 21941-913, Brazil
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7
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Liu Q, Shi C, Yu L, Zhang L, Xiong Y, Tian C. General order parameter based correlation analysis of protein backbone motions between experimental NMR relaxation measurements and molecular dynamics simulations. Biochem Biophys Res Commun 2015; 457:467-72. [PMID: 25600810 DOI: 10.1016/j.bbrc.2015.01.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Accepted: 01/07/2015] [Indexed: 11/30/2022]
Abstract
Internal backbone dynamic motions are essential for different protein functions and occur on a wide range of time scales, from femtoseconds to seconds. Molecular dynamic (MD) simulations and nuclear magnetic resonance (NMR) spin relaxation measurements are valuable tools to gain access to fast (nanosecond) internal motions. However, there exist few reports on correlation analysis between MD and NMR relaxation data. Here, backbone relaxation measurements of (15)N-labeled SH3 (Src homology 3) domain proteins in aqueous buffer were used to generate general order parameters (S(2)) using a model-free approach. Simultaneously, 80 ns MD simulations of SH3 domain proteins in a defined hydrated box at neutral pH were conducted and the general order parameters (S(2)) were derived from the MD trajectory. Correlation analysis using the Gromos force field indicated that S(2) values from NMR relaxation measurements and MD simulations were significantly different. MD simulations were performed on models with different charge states for three histidine residues, and with different water models, which were SPC (simple point charge) water model and SPC/E (extended simple point charge) water model. S(2) parameters from MD simulations with charges for all three histidines and with the SPC/E water model correlated well with S(2) calculated from the experimental NMR relaxation measurements, in a site-specific manner.
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Affiliation(s)
- Qing Liu
- Hefei National Laboratory for Physical Sciences at The Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026, PR China
| | - Chaowei Shi
- Hefei National Laboratory for Physical Sciences at The Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026, PR China
| | - Lu Yu
- Hefei National Laboratory for Physical Sciences at The Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026, PR China; High Magnetic Field Laboratory, Chinese Academy of Science, Hefei, Anhui, 230031, PR China
| | - Longhua Zhang
- Hefei National Laboratory for Physical Sciences at The Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026, PR China
| | - Ying Xiong
- Hefei National Laboratory for Physical Sciences at The Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026, PR China.
| | - Changlin Tian
- Hefei National Laboratory for Physical Sciences at The Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026, PR China; High Magnetic Field Laboratory, Chinese Academy of Science, Hefei, Anhui, 230031, PR China.
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8
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Abstract
Dynamical behaviors of glycosaminoglycans, as here illustrated with a hyaluronan oligosaccharide, are key regulators of biological functions.
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Affiliation(s)
- Vitor H. Pomin
- Program of Glycobiology
- Institute of Medical Biochemistry Leopoldo de Meis, and University Hospital Clementino Fraga Filho
- Federal University of Rio de Janeiro
- Rio de Janeiro, Brazil
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9
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Rösner HI, Kragelund BB. Structure and dynamic properties of membrane proteins using NMR. Compr Physiol 2013; 2:1491-539. [PMID: 23798308 DOI: 10.1002/cphy.c110036] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Integral membrane proteins are one of the most challenging groups of macromolecules despite their apparent conformational simplicity. They manage and drive transport, circulate information, and participate in cellular movements via interactions with other proteins and through intricate conformational changes. Their structural and functional decoding is challenging and has imposed demanding experimental development. Solution nuclear magnetic resonance (NMR) spectroscopy is one of the techniques providing the capacity to make a significant difference in the deciphering of the membrane protein structure-function paradigm. The method has evolved dramatically during the last decade resulting in a plethora of new experiments leading to a significant increase in the scientific repertoire for studying membrane proteins. Besides solving the three-dimensional structures using state-of-the-art approaches, a large variety of developments of well-established techniques are available providing insight into membrane protein flexibility, dynamics, and interactions. Inspired by the speed of development in the application of new strategies, by invention of methods to measure solvent accessibility and describe low-populated states, this review seeks to introduce the vast possibilities solution NMR can offer to the study of membrane protein structure-function analyses with special focus on applicability.
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Affiliation(s)
- Heike I Rösner
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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10
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The hepatitis B virus preS1 domain hijacks host trafficking proteins by motif mimicry. Nat Chem Biol 2013; 9:540-7. [PMID: 23851574 DOI: 10.1038/nchembio.1294] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Accepted: 06/12/2013] [Indexed: 01/05/2023]
Abstract
Hepatitis B virus (HBV) is an infectious, potentially lethal human pathogen. However, there are no effective therapies for chronic HBV infections. Antiviral development is hampered by the lack of high-resolution structures for essential HBV protein-protein interactions. The interaction between preS1, an HBV surface-protein domain, and its human binding partner, γ2-adaptin, subverts the membrane-trafficking apparatus to mediate virion export. This interaction is a putative drug target. We report here atomic-resolution descriptions of the binding thermodynamics and structural biology of the interaction between preS1 and the EAR domain of γ2-adaptin. NMR, protein engineering, X-ray crystallography and MS showed that preS1 contains multiple γ2-EAR-binding motifs that mimic the membrane-trafficking motifs (and binding modes) of host proteins. These motifs localize together to a relatively rigid, functionally important region of preS1, an intrinsically disordered protein. The preS1-γ2-EAR interaction was relatively weak and efficiently outcompeted by a synthetic peptide. Our data provide the structural road map for developing peptidomimetic antivirals targeting the γ2-EAR-preS1 interaction.
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11
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Repo H, Oeemig JS, Djupsjöbacka J, Iwaï H, Heikinheimo P. A monomeric TIM-barrel structure from Pyrococcus furiosus is optimized for extreme temperatures. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:1479-87. [PMID: 23090397 DOI: 10.1107/s0907444912037171] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Accepted: 08/28/2012] [Indexed: 11/10/2022]
Abstract
The structure of phosphoribosyl anthranilate isomerase (TrpF) from the hyperthermophilic archaeon Pyrococcus furiosus (PfTrpF) has been determined at 1.75 Å resolution. The PfTrpF structure has a monomeric TIM-barrel fold which differs from the dimeric structures of two other known thermophilic TrpF proteins. A comparison of the PfTrpF structure with the two known bacterial thermophilic TrpF structures and the structure of a related mesophilic protein from Escherichia coli (EcTrpF) is presented. The thermophilic TrpF structures contain a higher proportion of ion pairs and charged residues compared with the mesophilic EcTrpF. These residues contribute to the closure of the central barrel and the stabilization of the barrel and the surrounding α-helices. In the monomeric PfTrpF conserved structural water molecules are mostly absent; instead, the structural waters are replaced by direct side-chain-main-chain interactions. As a consequence of these combined mechanisms, the P. furiosus enzyme is a thermodynamically stable and entropically optimized monomeric TIM-barrel enzyme which defines a good framework for further protein engineering for industrial applications.
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Affiliation(s)
- Heidi Repo
- Institute of Biotechnology, University of Helsinki, PO Box 65, FI-00014 Helsinki, Finland
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12
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Sharma AK, Ye L, Alper SL, Rigby AC. Guanine nucleotides differentially modulate backbone dynamics of the STAS domain of the SulP/SLC26 transport protein Rv1739c of Mycobacterium tuberculosis. FEBS J 2011; 279:420-36. [PMID: 22118659 DOI: 10.1111/j.1742-4658.2011.08435.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Enzymatic catalysis and protein signaling are dynamic processes that involve local and/or global conformational changes occurring across a broad range of time scales. (1) H-(15) N relaxation NMR provides a comprehensive understanding of protein backbone dynamics both in the apo (unliganded) and ligand-bound conformations, enabling both fast and slow internal motions of individual amino acid residues to be observed. We recently reported the structure and nucleotide binding properties of the sulfate transporter and anti-sigma factor antagonist (STAS) domain of Rv1739c, a SulP anion transporter protein of Mycobacterium tuberculosis. In the present study, we report (1) H-(15) N NMR backbone dynamics measurements [longitudinal (T(1) ), transverse (T(2) ) and steady-state ({(1) H}-(15) N) heteronuclear NOE] of the Rv1739c STAS domain, in the absence and presence of saturating concentrations of GTP and GDP. Analysis of measured relaxation data and estimated dynamic parameters indicated distinct features differentiating the binding of GTP and GDP to Rv1739c STAS. The 9.55 ns overall rotational correlation time of Rv1739c STAS increased to 10.48 ns in the presence of GTP, and to 13.25 ns in the presence of GDP, indicating significant nucleotide-induced conformational changes. These conformational changes were accompanied by slow time scale (μs to ms) motions in discrete regions of the protein, as reflected by guanine nucleotide-induced changes in relaxation parameters. The observed nucleotide-specific alterations in the relaxation properties of individual STAS residues reflect an increased molecular anisotropy and/or the emergence of conformational equilibria governing functional properties of the STAS domain.
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Affiliation(s)
- Alok K Sharma
- Division of Molecular and Vascular Medicine, Renal Division, and Center for Vascular Biology Research, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
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13
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Savard PY, Daigle R, Morin S, Sebilo A, Meindre F, Lagüe P, Guertin M, Gagné SM. Structure and dynamics of Mycobacterium tuberculosis truncated hemoglobin N: insights from NMR spectroscopy and molecular dynamics simulations. Biochemistry 2011; 50:11121-30. [PMID: 21999759 DOI: 10.1021/bi201059a] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The potent nitric oxide dioxygenase (NOD) activity (trHbN-Fe²⁺-O₂ + (•)NO → trHbN-Fe³⁺-OH₂ + NO₃⁻) of Mycobacterium tuberculosis truncated hemoglobin N (trHbN) protects aerobic respiration from inhibition by (•)NO. The high activity of trHbN has been attributed in part to the presence of numerous short-lived hydrophobic cavities that allow partition and diffusion of the gaseous substrates (•)NO and O₂ to the active site. We investigated the relation between these cavities and the dynamics of the protein using solution NMR spectroscopy and molecular dynamics (MD). Results from both approaches indicate that the protein is mainly rigid with very limited motions of the backbone N-H bond vectors on the picoseconds-nanoseconds time scale, indicating that substrate diffusion and partition within trHbN may be controlled by side-chains movements. Model-free analysis also revealed the presence of slow motions (microseconds-milliseconds), not observed in MD simulations, for many residues located in helices B and G including the distal heme pocket Tyr33(B10). All currently known crystal structures and molecular dynamics data of truncated hemoglobins with the so-called pre-A N-terminal extension suggest a stable α-helical conformation that extends in solution. Moreover, a recent study attributed a crucial role to the pre-A helix for NOD activity. However, solution NMR data clearly show that in near-physiological conditions these residues do not adopt an α-helical conformation and are significantly disordered and that the helical conformation seen in crystal structures is likely induced by crystal contacts. Although this lack of order for the pre-A does not disagree with an important functional role for these residues, our data show that one should not assume an helical conformation for these residues in any functional interpretation. Moreover, future molecular dynamics simulations should not use an initial α-helical conformation for these residues in order to avoid a bias based on an erroneous initial structure for the N-termini residues. This work constitutes the first study of a truncated hemoglobin dynamics performed by solution heteronuclear relaxation NMR spectroscopy.
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Affiliation(s)
- Pierre-Yves Savard
- Département de biochimie, de microbiologie et de bio-informatique, Université Laval and PROTEO, Québec, Canada
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14
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Morin S. A practical guide to protein dynamics from 15N spin relaxation in solution. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2011; 59:245-62. [PMID: 21920220 DOI: 10.1016/j.pnmrs.2010.12.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2010] [Accepted: 12/17/2010] [Indexed: 05/08/2023]
Affiliation(s)
- Sébastien Morin
- Department of Structural Biology, Biozentrum, University of Basel, Switzerland.
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15
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Banerjee PR, Puttamadappa SS, Pande A, Shekhtman A, Pande J. Increased hydrophobicity and decreased backbone flexibility explain the lower solubility of a cataract-linked mutant of γD-crystallin. J Mol Biol 2011; 412:647-59. [PMID: 21827768 DOI: 10.1016/j.jmb.2011.07.058] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Revised: 07/22/2011] [Accepted: 07/25/2011] [Indexed: 11/18/2022]
Abstract
A number of point mutations in γD-crystallin are associated with human cataract. The Pro23-to-Thr (P23T) mutation is perhaps the most common, is geographically widespread, and presents itself in a variety of phenotypes. It is therefore important to understand the molecular basis of lens opacity due to this mutation. In our earlier studies, we noted that P23T shows retrograde and sharply lowered solubility, most likely due to the emergence of hydrophobic patches involved in protein aggregation. Binding of 4,4'-dianilino-1,1'-binaphthyl-5,5'-disulfonate (Bis-ANS) dye (a probe commonly used for detecting surface hydrophobicity) competed with aggregation, suggesting that the residues involved in Bis-ANS binding are also involved in protein aggregation. Here, using NMR spectroscopy in conjunction with Bis-ANS binding, we identify three residues (Y16, D21, and Y50) in P23T that are involved in binding the dye. Furthermore, using (15)N NMR relaxation experiments, we show that, in the mutant protein, backbone fluctuations are restricted to the picosecond-to-nanosecond and microsecond timescales relative to the wild type. Our present studies specify the residues involved in these two pivotal characteristics of the mutant protein, namely increased surface hydrophobicity and restricted mobility of the protein backbone, which can explain the nucleation and further propagation of protein aggregates. Thus, we have now identified the residues in the P23T mutant that give rise to novel hydrophobic surfaces, as well as those regions of the protein backbone where fluctuations in different timescales are restricted, providing a comprehensive understanding of how lens opacity could result from this mutation.
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Affiliation(s)
- Priya R Banerjee
- Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA
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Nørholm AB, Hendus-Altenburger R, Bjerre G, Kjaergaard M, Pedersen SF, Kragelund BB. The Intracellular Distal Tail of the Na+/H+ Exchanger NHE1 Is Intrinsically Disordered: Implications for NHE1 Trafficking. Biochemistry 2011; 50:3469-80. [DOI: 10.1021/bi1019989] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ann-Beth Nørholm
- Cell and Developmental Biology, Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100 Copenhagen Ø, Denmark
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Ruth Hendus-Altenburger
- Cell and Developmental Biology, Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100 Copenhagen Ø, Denmark
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Gabriel Bjerre
- Cell and Developmental Biology, Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100 Copenhagen Ø, Denmark
| | - Magnus Kjaergaard
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Stine F. Pedersen
- Cell and Developmental Biology, Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100 Copenhagen Ø, Denmark
| | - Birthe B. Kragelund
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
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Ishima R. Recent developments in (15)N NMR relaxation studies that probe protein backbone dynamics. Top Curr Chem (Cham) 2011; 326:99-122. [PMID: 21898206 DOI: 10.1007/128_2011_212] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nuclear Magnetic Resonance (NMR) relaxation is a powerful technique that provides information about internal dynamics associated with configurational energetics in proteins, as well as site-specific information involved in conformational equilibria. In particular, (15)N relaxation is a useful probe to characterize overall and internal backbone dynamics of proteins because the relaxation mainly reflects reorientational motion of the N-H bond vector. Over the past 20 years, experiments and protocols for analysis of (15)N R (1), R 2, and the heteronuclear (15)N-{(1)H} NOE data have been well established. The development of these methods has kept pace with the increase in the available static-magnetic field strength, providing dynamic parameters optimized from data fitting at multiple field strengths. Using these methodological advances, correlation times for global tumbling and order parameters and correlation times for internal motions of many proteins have been determined. More recently, transverse relaxation dispersion experiments have extended the range of NMR relaxation studies to the milli- to microsecond time scale, and have provided quantitative information about functional conformational exchange in proteins. Here, we present an overview of recent advances in (15)N relaxation experiments to characterize protein backbone dynamics.
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Affiliation(s)
- Rieko Ishima
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA.
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